Analysis output: all-atom contacts and geometry for 5uke_trimmedH.pdb

Model-by-model validation results

Summary statistics for m01_5uke_trimmedH.pdb

All-Atom
Contacts Clashscore, all atoms: 19.78 33^rd percentile^* (N=1784, all resolutions)

Clashscore is the number of serious steric overlaps (> 0.4 Å) per 1000 atoms.

Protein
Geometry Poor rotamers 10 10.10% Goal: <0.3%

Favored rotamers 80 80.81% Goal: >98%

Ramachandran outliers 3 2.46% Goal: <0.05%

Ramachandran favored 111 90.98% Goal: >98%

Rama distribution Z-score -2.20 ± 0.63 Goal: abs(Z score) < 2

MolProbity score^{^} 3.07 20^th percentile^* (N=27675, 0Å - 99Å)

Cβ deviations >0.25Å 0 0.00% Goal: 0

Bad bonds: 0 / 963 0.00% Goal: 0%

Bad angles: 0 / 1302 0.00% Goal: <0.1%

Peptide Omegas Cis Prolines: 0 / 3 0.00% Expected: ≤1 per chain, or ≤5%

Low-resolution Criteria CaBLAM outliers 8 6.7% Goal: <1.0%

CA Geometry outliers 4 3.33% Goal: <0.5%

Additional validations Chiral volume outliers 0/142
Waters with clashes 0/0 0.00% See UnDowser table for details
In the two column results, the left column gives the raw count, right column gives the percentage.
* 100^th percentile is the best among structures of comparable resolution; 0^th percentile is the worst. For clashscore the comparative set of structures was selected in 2004, for MolProbity score in 2006.
^{^} MolProbity score combines the clashscore, rotamer, and Ramachandran evaluations into a single score, normalized to be on the same scale as X-ray resolution.
Key to table colors and cutoffs here:

Multi-criterion visualizations

View (82 Kb)

View (2.8 Kb)

Single-criterion visualizations

Clash list (1.7 Kb): View
Ramachandran plot kinemage (412 Kb): View in KiNG | View in NGL | Download
Ramachandran plot PDF (1.7 Mb): View
Ramachandran distribution Z-score analysis (7.2 Kb): View
Chiral volume report (788 bytes): View
Cβ deviation scatter plot (14 Kb): View in KiNG | View in NGL | Download

Summary statistics for m02_5uke_trimmedH.pdb

All-Atom
Contacts Clashscore, all atoms: 17.1 41^st percentile^* (N=1784, all resolutions)

Clashscore is the number of serious steric overlaps (> 0.4 Å) per 1000 atoms.

Protein
Geometry Poor rotamers 9 9.09% Goal: <0.3%

Favored rotamers 82 82.83% Goal: >98%

Ramachandran outliers 3 2.46% Goal: <0.05%

Ramachandran favored 110 90.16% Goal: >98%

Rama distribution Z-score -1.73 ± 0.68 Goal: abs(Z score) < 2

MolProbity score^{^} 3.01 23^rd percentile^* (N=27675, 0Å - 99Å)

Cβ deviations >0.25Å 0 0.00% Goal: 0

Bad bonds: 0 / 963 0.00% Goal: 0%

Bad angles: 0 / 1302 0.00% Goal: <0.1%

Peptide Omegas Cis Prolines: 0 / 3 0.00% Expected: ≤1 per chain, or ≤5%

Low-resolution Criteria CaBLAM outliers 13 10.8% Goal: <1.0%

CA Geometry outliers 3 2.50% Goal: <0.5%

Additional validations Chiral volume outliers 0/142
Waters with clashes 0/0 0.00% See UnDowser table for details
In the two column results, the left column gives the raw count, right column gives the percentage.
* 100^th percentile is the best among structures of comparable resolution; 0^th percentile is the worst. For clashscore the comparative set of structures was selected in 2004, for MolProbity score in 2006.
^{^} MolProbity score combines the clashscore, rotamer, and Ramachandran evaluations into a single score, normalized to be on the same scale as X-ray resolution.
Key to table colors and cutoffs here:

Multi-criterion visualizations

View (78 Kb)

View (2.8 Kb)

Single-criterion visualizations

Clash list (1.5 Kb): View
Ramachandran plot kinemage (412 Kb): View in KiNG | View in NGL | Download
Ramachandran plot PDF (1.7 Mb): View
Ramachandran distribution Z-score analysis (7.2 Kb): View
Chiral volume report (788 bytes): View
Cβ deviation scatter plot (14 Kb): View in KiNG | View in NGL | Download

Summary statistics for m03_5uke_trimmedH.pdb

All-Atom
Contacts Clashscore, all atoms: 18.17 37^th percentile^* (N=1784, all resolutions)

Clashscore is the number of serious steric overlaps (> 0.4 Å) per 1000 atoms.

Protein
Geometry Poor rotamers 9 9.09% Goal: <0.3%

Favored rotamers 85 85.86% Goal: >98%

Ramachandran outliers 3 2.46% Goal: <0.05%

Ramachandran favored 109 89.34% Goal: >98%

Rama distribution Z-score -1.33 ± 0.68 Goal: abs(Z score) < 2

MolProbity score^{^} 3.05 21^st percentile^* (N=27675, 0Å - 99Å)

Cβ deviations >0.25Å 0 0.00% Goal: 0

Bad bonds: 0 / 963 0.00% Goal: 0%

Bad angles: 0 / 1302 0.00% Goal: <0.1%

Peptide Omegas Cis Prolines: 0 / 3 0.00% Expected: ≤1 per chain, or ≤5%

Low-resolution Criteria CaBLAM outliers 9 7.5% Goal: <1.0%

CA Geometry outliers 2 1.67% Goal: <0.5%

Additional validations Chiral volume outliers 0/142
Waters with clashes 0/0 0.00% See UnDowser table for details
In the two column results, the left column gives the raw count, right column gives the percentage.
* 100^th percentile is the best among structures of comparable resolution; 0^th percentile is the worst. For clashscore the comparative set of structures was selected in 2004, for MolProbity score in 2006.
^{^} MolProbity score combines the clashscore, rotamer, and Ramachandran evaluations into a single score, normalized to be on the same scale as X-ray resolution.
Key to table colors and cutoffs here:

Multi-criterion visualizations

View (72 Kb)

View (2.8 Kb)

Single-criterion visualizations

Clash list (1.6 Kb): View
Ramachandran plot kinemage (412 Kb): View in KiNG | View in NGL | Download
Ramachandran plot PDF (1.7 Mb): View
Ramachandran distribution Z-score analysis (7.2 Kb): View
Chiral volume report (788 bytes): View
Cβ deviation scatter plot (14 Kb): View in KiNG | View in NGL | Download

Summary statistics for m04_5uke_trimmedH.pdb

All-Atom
Contacts Clashscore, all atoms: 20.84 30^th percentile^* (N=1784, all resolutions)

Clashscore is the number of serious steric overlaps (> 0.4 Å) per 1000 atoms.

Protein
Geometry Poor rotamers 8 8.08% Goal: <0.3%

Favored rotamers 82 82.83% Goal: >98%

Ramachandran outliers 3 2.46% Goal: <0.05%

Ramachandran favored 110 90.16% Goal: >98%

Rama distribution Z-score -1.83 ± 0.66 Goal: abs(Z score) < 2

MolProbity score^{^} 3.05 21^st percentile^* (N=27675, 0Å - 99Å)

Cβ deviations >0.25Å 0 0.00% Goal: 0

Bad bonds: 0 / 963 0.00% Goal: 0%

Bad angles: 0 / 1302 0.00% Goal: <0.1%

Peptide Omegas Cis Prolines: 0 / 3 0.00% Expected: ≤1 per chain, or ≤5%

Low-resolution Criteria CaBLAM outliers 10 8.3% Goal: <1.0%

CA Geometry outliers 2 1.67% Goal: <0.5%

Additional validations Chiral volume outliers 0/142
Waters with clashes 0/0 0.00% See UnDowser table for details
In the two column results, the left column gives the raw count, right column gives the percentage.
* 100^th percentile is the best among structures of comparable resolution; 0^th percentile is the worst. For clashscore the comparative set of structures was selected in 2004, for MolProbity score in 2006.
^{^} MolProbity score combines the clashscore, rotamer, and Ramachandran evaluations into a single score, normalized to be on the same scale as X-ray resolution.
Key to table colors and cutoffs here:

Multi-criterion visualizations

View (78 Kb)

View (2.8 Kb)

Single-criterion visualizations

Clash list (1.8 Kb): View
Ramachandran plot kinemage (412 Kb): View in KiNG | View in NGL | Download
Ramachandran plot PDF (1.7 Mb): View
Ramachandran distribution Z-score analysis (7.2 Kb): View
Chiral volume report (788 bytes): View
Cβ deviation scatter plot (14 Kb): View in KiNG | View in NGL | Download

Summary statistics for m05_5uke_trimmedH.pdb

All-Atom
Contacts Clashscore, all atoms: 22.98 25^th percentile^* (N=1784, all resolutions)

Clashscore is the number of serious steric overlaps (> 0.4 Å) per 1000 atoms.

Protein
Geometry Poor rotamers 8 8.08% Goal: <0.3%

Favored rotamers 85 85.86% Goal: >98%

Ramachandran outliers 3 2.46% Goal: <0.05%

Ramachandran favored 107 87.70% Goal: >98%

Rama distribution Z-score -1.99 ± 0.67 Goal: abs(Z score) < 2

MolProbity score^{^} 3.15 18^th percentile^* (N=27675, 0Å - 99Å)

Cβ deviations >0.25Å 0 0.00% Goal: 0

Bad bonds: 0 / 963 0.00% Goal: 0%

Bad angles: 0 / 1302 0.00% Goal: <0.1%

Peptide Omegas Cis Prolines: 0 / 3 0.00% Expected: ≤1 per chain, or ≤5%

Low-resolution Criteria CaBLAM outliers 10 8.3% Goal: <1.0%

CA Geometry outliers 3 2.50% Goal: <0.5%

Additional validations Chiral volume outliers 0/142
Waters with clashes 0/0 0.00% See UnDowser table for details
In the two column results, the left column gives the raw count, right column gives the percentage.
* 100^th percentile is the best among structures of comparable resolution; 0^th percentile is the worst. For clashscore the comparative set of structures was selected in 2004, for MolProbity score in 2006.
^{^} MolProbity score combines the clashscore, rotamer, and Ramachandran evaluations into a single score, normalized to be on the same scale as X-ray resolution.
Key to table colors and cutoffs here:

Multi-criterion visualizations

View (83 Kb)

View (2.8 Kb)

Single-criterion visualizations

Clash list (1.9 Kb): View
Ramachandran plot kinemage (412 Kb): View in KiNG | View in NGL | Download
Ramachandran plot PDF (1.7 Mb): View
Ramachandran distribution Z-score analysis (7.2 Kb): View
Chiral volume report (788 bytes): View
Cβ deviation scatter plot (14 Kb): View in KiNG | View in NGL | Download

Summary statistics for m06_5uke_trimmedH.pdb

All-Atom
Contacts Clashscore, all atoms: 19.78 33^rd percentile^* (N=1784, all resolutions)

Clashscore is the number of serious steric overlaps (> 0.4 Å) per 1000 atoms.

Protein
Geometry Poor rotamers 7 7.07% Goal: <0.3%

Favored rotamers 85 85.86% Goal: >98%

Ramachandran outliers 2 1.64% Goal: <0.05%

Ramachandran favored 110 90.16% Goal: >98%

Rama distribution Z-score -2.06 ± 0.63 Goal: abs(Z score) < 2

MolProbity score^{^} 2.98 24^th percentile^* (N=27675, 0Å - 99Å)

Cβ deviations >0.25Å 0 0.00% Goal: 0

Bad bonds: 0 / 963 0.00% Goal: 0%

Bad angles: 0 / 1302 0.00% Goal: <0.1%

Peptide Omegas Cis Prolines: 0 / 3 0.00% Expected: ≤1 per chain, or ≤5%

Low-resolution Criteria CaBLAM outliers 10 8.3% Goal: <1.0%

CA Geometry outliers 3 2.50% Goal: <0.5%

Additional validations Chiral volume outliers 0/142
Waters with clashes 0/0 0.00% See UnDowser table for details
In the two column results, the left column gives the raw count, right column gives the percentage.
* 100^th percentile is the best among structures of comparable resolution; 0^th percentile is the worst. For clashscore the comparative set of structures was selected in 2004, for MolProbity score in 2006.
^{^} MolProbity score combines the clashscore, rotamer, and Ramachandran evaluations into a single score, normalized to be on the same scale as X-ray resolution.
Key to table colors and cutoffs here:

Multi-criterion visualizations

View (89 Kb)

View (2.8 Kb)

Single-criterion visualizations

Clash list (1.7 Kb): View
Ramachandran plot kinemage (412 Kb): View in KiNG | View in NGL | Download
Ramachandran plot PDF (1.7 Mb): View
Ramachandran distribution Z-score analysis (7.2 Kb): View
Chiral volume report (788 bytes): View
Cβ deviation scatter plot (14 Kb): View in KiNG | View in NGL | Download

Summary statistics for m07_5uke_trimmedH.pdb

All-Atom
Contacts Clashscore, all atoms: 26.72 18^th percentile^* (N=1784, all resolutions)

Clashscore is the number of serious steric overlaps (> 0.4 Å) per 1000 atoms.

Protein
Geometry Poor rotamers 11 11.11% Goal: <0.3%

Favored rotamers 81 81.82% Goal: >98%

Ramachandran outliers 3 2.46% Goal: <0.05%

Ramachandran favored 108 88.52% Goal: >98%

Rama distribution Z-score -1.53 ± 0.70 Goal: abs(Z score) < 2

MolProbity score^{^} 3.30 13^th percentile^* (N=27675, 0Å - 99Å)

Cβ deviations >0.25Å 0 0.00% Goal: 0

Bad bonds: 0 / 963 0.00% Goal: 0%

Bad angles: 0 / 1302 0.00% Goal: <0.1%

Peptide Omegas Cis Prolines: 0 / 3 0.00% Expected: ≤1 per chain, or ≤5%

Low-resolution Criteria CaBLAM outliers 10 8.3% Goal: <1.0%

CA Geometry outliers 3 2.50% Goal: <0.5%

Additional validations Chiral volume outliers 0/142
Waters with clashes 0/0 0.00% See UnDowser table for details
In the two column results, the left column gives the raw count, right column gives the percentage.
* 100^th percentile is the best among structures of comparable resolution; 0^th percentile is the worst. For clashscore the comparative set of structures was selected in 2004, for MolProbity score in 2006.
^{^} MolProbity score combines the clashscore, rotamer, and Ramachandran evaluations into a single score, normalized to be on the same scale as X-ray resolution.
Key to table colors and cutoffs here:

Multi-criterion visualizations

View (94 Kb)

View (2.8 Kb)

Single-criterion visualizations

Clash list (2.2 Kb): View
Ramachandran plot kinemage (412 Kb): View in KiNG | View in NGL | Download
Ramachandran plot PDF (1.7 Mb): View
Ramachandran distribution Z-score analysis (7.2 Kb): View
Chiral volume report (788 bytes): View
Cβ deviation scatter plot (14 Kb): View in KiNG | View in NGL | Download

Summary statistics for m08_5uke_trimmedH.pdb

All-Atom
Contacts Clashscore, all atoms: 22.45 26^th percentile^* (N=1784, all resolutions)

Clashscore is the number of serious steric overlaps (> 0.4 Å) per 1000 atoms.

Protein
Geometry Poor rotamers 9 9.09% Goal: <0.3%

Favored rotamers 81 81.82% Goal: >98%

Ramachandran outliers 3 2.46% Goal: <0.05%

Ramachandran favored 105 86.07% Goal: >98%

Rama distribution Z-score -2.00 ± 0.72 Goal: abs(Z score) < 2

MolProbity score^{^} 3.21 16^th percentile^* (N=27675, 0Å - 99Å)

Cβ deviations >0.25Å 0 0.00% Goal: 0

Bad bonds: 0 / 963 0.00% Goal: 0%

Bad angles: 0 / 1302 0.00% Goal: <0.1%

Peptide Omegas Cis Prolines: 0 / 3 0.00% Expected: ≤1 per chain, or ≤5%

Low-resolution Criteria CaBLAM outliers 12 10.0% Goal: <1.0%

CA Geometry outliers 3 2.50% Goal: <0.5%

Additional validations Chiral volume outliers 0/142
Waters with clashes 0/0 0.00% See UnDowser table for details
In the two column results, the left column gives the raw count, right column gives the percentage.
* 100^th percentile is the best among structures of comparable resolution; 0^th percentile is the worst. For clashscore the comparative set of structures was selected in 2004, for MolProbity score in 2006.
^{^} MolProbity score combines the clashscore, rotamer, and Ramachandran evaluations into a single score, normalized to be on the same scale as X-ray resolution.
Key to table colors and cutoffs here:

Multi-criterion visualizations

View (92 Kb)

View (2.8 Kb)

Single-criterion visualizations

Clash list (1.9 Kb): View
Ramachandran plot kinemage (412 Kb): View in KiNG | View in NGL | Download
Ramachandran plot PDF (1.7 Mb): View
Ramachandran distribution Z-score analysis (7.2 Kb): View
Chiral volume report (788 bytes): View
Cβ deviation scatter plot (14 Kb): View in KiNG | View in NGL | Download

Summary statistics for m09_5uke_trimmedH.pdb

All-Atom
Contacts Clashscore, all atoms: 22.98 25^th percentile^* (N=1784, all resolutions)

Clashscore is the number of serious steric overlaps (> 0.4 Å) per 1000 atoms.

Protein
Geometry Poor rotamers 9 9.09% Goal: <0.3%

Favored rotamers 84 84.85% Goal: >98%

Ramachandran outliers 3 2.46% Goal: <0.05%

Ramachandran favored 110 90.16% Goal: >98%

Rama distribution Z-score -0.88 ± 0.69 Goal: abs(Z score) < 2

MolProbity score^{^} 3.13 18^th percentile^* (N=27675, 0Å - 99Å)

Cβ deviations >0.25Å 0 0.00% Goal: 0

Bad bonds: 0 / 963 0.00% Goal: 0%

Bad angles: 0 / 1302 0.00% Goal: <0.1%

Peptide Omegas Cis Prolines: 0 / 3 0.00% Expected: ≤1 per chain, or ≤5%

Low-resolution Criteria CaBLAM outliers 9 7.5% Goal: <1.0%

CA Geometry outliers 2 1.67% Goal: <0.5%

Additional validations Chiral volume outliers 0/142
Waters with clashes 0/0 0.00% See UnDowser table for details
In the two column results, the left column gives the raw count, right column gives the percentage.
* 100^th percentile is the best among structures of comparable resolution; 0^th percentile is the worst. For clashscore the comparative set of structures was selected in 2004, for MolProbity score in 2006.
^{^} MolProbity score combines the clashscore, rotamer, and Ramachandran evaluations into a single score, normalized to be on the same scale as X-ray resolution.
Key to table colors and cutoffs here:

Multi-criterion visualizations

View (83 Kb)

View (2.8 Kb)

Single-criterion visualizations

Clash list (1.9 Kb): View
Ramachandran plot kinemage (412 Kb): View in KiNG | View in NGL | Download
Ramachandran plot PDF (1.7 Mb): View
Ramachandran distribution Z-score analysis (7.2 Kb): View
Chiral volume report (788 bytes): View
Cβ deviation scatter plot (14 Kb): View in KiNG | View in NGL | Download

Summary statistics for m10_5uke_trimmedH.pdb

All-Atom
Contacts Clashscore, all atoms: 24.59 22^nd percentile^* (N=1784, all resolutions)

Clashscore is the number of serious steric overlaps (> 0.4 Å) per 1000 atoms.

Protein
Geometry Poor rotamers 12 12.12% Goal: <0.3%

Favored rotamers 80 80.81% Goal: >98%

Ramachandran outliers 3 2.46% Goal: <0.05%

Ramachandran favored 110 90.16% Goal: >98%

Rama distribution Z-score -1.49 ± 0.68 Goal: abs(Z score) < 2

MolProbity score^{^} 3.25 15^th percentile^* (N=27675, 0Å - 99Å)

Cβ deviations >0.25Å 0 0.00% Goal: 0

Bad bonds: 0 / 963 0.00% Goal: 0%

Bad angles: 0 / 1302 0.00% Goal: <0.1%

Peptide Omegas Cis Prolines: 0 / 3 0.00% Expected: ≤1 per chain, or ≤5%

Low-resolution Criteria CaBLAM outliers 9 7.5% Goal: <1.0%

CA Geometry outliers 2 1.67% Goal: <0.5%

Additional validations Chiral volume outliers 0/142
Waters with clashes 0/0 0.00% See UnDowser table for details
In the two column results, the left column gives the raw count, right column gives the percentage.
* 100^th percentile is the best among structures of comparable resolution; 0^th percentile is the worst. For clashscore the comparative set of structures was selected in 2004, for MolProbity score in 2006.
^{^} MolProbity score combines the clashscore, rotamer, and Ramachandran evaluations into a single score, normalized to be on the same scale as X-ray resolution.
Key to table colors and cutoffs here:

Multi-criterion visualizations

View (89 Kb)

View (2.8 Kb)

Single-criterion visualizations

Clash list (2.1 Kb): View
Ramachandran plot kinemage (412 Kb): View in KiNG | View in NGL | Download
Ramachandran plot PDF (1.7 Mb): View
Ramachandran distribution Z-score analysis (7.2 Kb): View
Chiral volume report (788 bytes): View
Cβ deviation scatter plot (14 Kb): View in KiNG | View in NGL | Download

Summary statistics for m11_5uke_trimmedH.pdb

All-Atom
Contacts Clashscore, all atoms: 19.78 33^rd percentile^* (N=1784, all resolutions)

Clashscore is the number of serious steric overlaps (> 0.4 Å) per 1000 atoms.

Protein
Geometry Poor rotamers 11 11.11% Goal: <0.3%

Favored rotamers 78 78.79% Goal: >98%

Ramachandran outliers 3 2.46% Goal: <0.05%

Ramachandran favored 106 86.89% Goal: >98%

Rama distribution Z-score -1.75 ± 0.69 Goal: abs(Z score) < 2

MolProbity score^{^} 3.21 16^th percentile^* (N=27675, 0Å - 99Å)

Cβ deviations >0.25Å 0 0.00% Goal: 0

Bad bonds: 0 / 963 0.00% Goal: 0%

Bad angles: 0 / 1302 0.00% Goal: <0.1%

Peptide Omegas Cis Prolines: 0 / 3 0.00% Expected: ≤1 per chain, or ≤5%

Low-resolution Criteria CaBLAM outliers 10 8.3% Goal: <1.0%

CA Geometry outliers 2 1.67% Goal: <0.5%

Additional validations Chiral volume outliers 0/142
Waters with clashes 0/0 0.00% See UnDowser table for details
In the two column results, the left column gives the raw count, right column gives the percentage.
* 100^th percentile is the best among structures of comparable resolution; 0^th percentile is the worst. For clashscore the comparative set of structures was selected in 2004, for MolProbity score in 2006.
^{^} MolProbity score combines the clashscore, rotamer, and Ramachandran evaluations into a single score, normalized to be on the same scale as X-ray resolution.
Key to table colors and cutoffs here:

Multi-criterion visualizations

View (77 Kb)

View (2.8 Kb)

Single-criterion visualizations

Clash list (1.7 Kb): View
Ramachandran plot kinemage (412 Kb): View in KiNG | View in NGL | Download
Ramachandran plot PDF (1.7 Mb): View
Ramachandran distribution Z-score analysis (7.2 Kb): View
Chiral volume report (788 bytes): View
Cβ deviation scatter plot (14 Kb): View in KiNG | View in NGL | Download

Summary statistics for m12_5uke_trimmedH.pdb

All-Atom
Contacts Clashscore, all atoms: 22.98 25^th percentile^* (N=1784, all resolutions)

Clashscore is the number of serious steric overlaps (> 0.4 Å) per 1000 atoms.

Protein
Geometry Poor rotamers 11 11.11% Goal: <0.3%

Favored rotamers 85 85.86% Goal: >98%

Ramachandran outliers 3 2.46% Goal: <0.05%

Ramachandran favored 109 89.34% Goal: >98%

Rama distribution Z-score -1.93 ± 0.67 Goal: abs(Z score) < 2

MolProbity score^{^} 3.21 16^th percentile^* (N=27675, 0Å - 99Å)

Cβ deviations >0.25Å 0 0.00% Goal: 0

Bad bonds: 0 / 963 0.00% Goal: 0%

Bad angles: 0 / 1302 0.00% Goal: <0.1%

Peptide Omegas Cis Prolines: 0 / 3 0.00% Expected: ≤1 per chain, or ≤5%

Low-resolution Criteria CaBLAM outliers 9 7.5% Goal: <1.0%

CA Geometry outliers 2 1.67% Goal: <0.5%

Additional validations Chiral volume outliers 0/142
Waters with clashes 0/0 0.00% See UnDowser table for details
In the two column results, the left column gives the raw count, right column gives the percentage.
* 100^th percentile is the best among structures of comparable resolution; 0^th percentile is the worst. For clashscore the comparative set of structures was selected in 2004, for MolProbity score in 2006.
^{^} MolProbity score combines the clashscore, rotamer, and Ramachandran evaluations into a single score, normalized to be on the same scale as X-ray resolution.
Key to table colors and cutoffs here:

Multi-criterion visualizations

View (83 Kb)

View (2.8 Kb)

Single-criterion visualizations

Clash list (1.9 Kb): View
Ramachandran plot kinemage (412 Kb): View in KiNG | View in NGL | Download
Ramachandran plot PDF (1.7 Mb): View
Ramachandran distribution Z-score analysis (7.2 Kb): View
Chiral volume report (788 bytes): View
Cβ deviation scatter plot (14 Kb): View in KiNG | View in NGL | Download

Summary statistics for m13_5uke_trimmedH.pdb

All-Atom
Contacts Clashscore, all atoms: 19.24 35^th percentile^* (N=1784, all resolutions)

Clashscore is the number of serious steric overlaps (> 0.4 Å) per 1000 atoms.

Protein
Geometry Poor rotamers 10 10.10% Goal: <0.3%

Favored rotamers 80 80.81% Goal: >98%

Ramachandran outliers 3 2.46% Goal: <0.05%

Ramachandran favored 106 86.89% Goal: >98%

Rama distribution Z-score -2.15 ± 0.69 Goal: abs(Z score) < 2

MolProbity score^{^} 3.17 17^th percentile^* (N=27675, 0Å - 99Å)

Cβ deviations >0.25Å 0 0.00% Goal: 0

Bad bonds: 0 / 963 0.00% Goal: 0%

Bad angles: 0 / 1302 0.00% Goal: <0.1%

Peptide Omegas Cis Prolines: 0 / 3 0.00% Expected: ≤1 per chain, or ≤5%

Low-resolution Criteria CaBLAM outliers 7 5.8% Goal: <1.0%

CA Geometry outliers 2 1.67% Goal: <0.5%

Additional validations Chiral volume outliers 0/142
Waters with clashes 0/0 0.00% See UnDowser table for details
In the two column results, the left column gives the raw count, right column gives the percentage.
* 100^th percentile is the best among structures of comparable resolution; 0^th percentile is the worst. For clashscore the comparative set of structures was selected in 2004, for MolProbity score in 2006.
^{^} MolProbity score combines the clashscore, rotamer, and Ramachandran evaluations into a single score, normalized to be on the same scale as X-ray resolution.
Key to table colors and cutoffs here:

Multi-criterion visualizations

View (84 Kb)

View (2.8 Kb)

Single-criterion visualizations

Clash list (1.7 Kb): View
Ramachandran plot kinemage (412 Kb): View in KiNG | View in NGL | Download
Ramachandran plot PDF (1.7 Mb): View
Ramachandran distribution Z-score analysis (7.2 Kb): View
Chiral volume report (788 bytes): View
Cβ deviation scatter plot (14 Kb): View in KiNG | View in NGL | Download

Summary statistics for m14_5uke_trimmedH.pdb

All-Atom
Contacts Clashscore, all atoms: 24.05 23^rd percentile^* (N=1784, all resolutions)

Clashscore is the number of serious steric overlaps (> 0.4 Å) per 1000 atoms.

Protein
Geometry Poor rotamers 10 10.10% Goal: <0.3%

Favored rotamers 80 80.81% Goal: >98%

Ramachandran outliers 3 2.46% Goal: <0.05%

Ramachandran favored 107 87.70% Goal: >98%

Rama distribution Z-score -1.80 ± 0.68 Goal: abs(Z score) < 2

MolProbity score^{^} 3.24 15^th percentile^* (N=27675, 0Å - 99Å)

Cβ deviations >0.25Å 0 0.00% Goal: 0

Bad bonds: 0 / 963 0.00% Goal: 0%

Bad angles: 0 / 1302 0.00% Goal: <0.1%

Peptide Omegas Cis Prolines: 0 / 3 0.00% Expected: ≤1 per chain, or ≤5%

Low-resolution Criteria CaBLAM outliers 10 8.3% Goal: <1.0%

CA Geometry outliers 4 3.33% Goal: <0.5%

Additional validations Chiral volume outliers 0/142
Waters with clashes 0/0 0.00% See UnDowser table for details
In the two column results, the left column gives the raw count, right column gives the percentage.
* 100^th percentile is the best among structures of comparable resolution; 0^th percentile is the worst. For clashscore the comparative set of structures was selected in 2004, for MolProbity score in 2006.
^{^} MolProbity score combines the clashscore, rotamer, and Ramachandran evaluations into a single score, normalized to be on the same scale as X-ray resolution.
Key to table colors and cutoffs here:

Multi-criterion visualizations

View (95 Kb)

View (2.8 Kb)

Single-criterion visualizations

Clash list (2 Kb): View
Ramachandran plot kinemage (412 Kb): View in KiNG | View in NGL | Download
Ramachandran plot PDF (1.7 Mb): View
Ramachandran distribution Z-score analysis (7.2 Kb): View
Chiral volume report (788 bytes): View
Cβ deviation scatter plot (14 Kb): View in KiNG | View in NGL | Download

Summary statistics for m15_5uke_trimmedH.pdb

All-Atom
Contacts Clashscore, all atoms: 20.84 30^th percentile^* (N=1784, all resolutions)

Clashscore is the number of serious steric overlaps (> 0.4 Å) per 1000 atoms.

Protein
Geometry Poor rotamers 9 9.09% Goal: <0.3%

Favored rotamers 81 81.82% Goal: >98%

Ramachandran outliers 2 1.64% Goal: <0.05%

Ramachandran favored 110 90.16% Goal: >98%

Rama distribution Z-score -2.29 ± 0.66 Goal: abs(Z score) < 2

MolProbity score^{^} 3.09 20^th percentile^* (N=27675, 0Å - 99Å)

Cβ deviations >0.25Å 0 0.00% Goal: 0

Bad bonds: 0 / 963 0.00% Goal: 0%

Bad angles: 0 / 1302 0.00% Goal: <0.1%

Peptide Omegas Cis Prolines: 0 / 3 0.00% Expected: ≤1 per chain, or ≤5%

Low-resolution Criteria CaBLAM outliers 10 8.3% Goal: <1.0%

CA Geometry outliers 2 1.67% Goal: <0.5%

Additional validations Chiral volume outliers 0/142
Waters with clashes 0/0 0.00% See UnDowser table for details
In the two column results, the left column gives the raw count, right column gives the percentage.
* 100^th percentile is the best among structures of comparable resolution; 0^th percentile is the worst. For clashscore the comparative set of structures was selected in 2004, for MolProbity score in 2006.
^{^} MolProbity score combines the clashscore, rotamer, and Ramachandran evaluations into a single score, normalized to be on the same scale as X-ray resolution.
Key to table colors and cutoffs here:

Multi-criterion visualizations

View (81 Kb)

View (2.8 Kb)

Single-criterion visualizations

Clash list (1.8 Kb): View
Ramachandran plot kinemage (412 Kb): View in KiNG | View in NGL | Download
Ramachandran plot PDF (1.7 Mb): View
Ramachandran distribution Z-score analysis (7.2 Kb): View
Chiral volume report (788 bytes): View
Cβ deviation scatter plot (14 Kb): View in KiNG | View in NGL | Download

Summary statistics for m16_5uke_trimmedH.pdb

All-Atom
Contacts Clashscore, all atoms: 18.17 37^th percentile^* (N=1784, all resolutions)

Clashscore is the number of serious steric overlaps (> 0.4 Å) per 1000 atoms.

Protein
Geometry Poor rotamers 8 8.08% Goal: <0.3%

Favored rotamers 82 82.83% Goal: >98%

Ramachandran outliers 4 3.28% Goal: <0.05%

Ramachandran favored 107 87.70% Goal: >98%

Rama distribution Z-score -1.85 ± 0.72 Goal: abs(Z score) < 2

MolProbity score^{^} 3.05 21^st percentile^* (N=27675, 0Å - 99Å)

Cβ deviations >0.25Å 0 0.00% Goal: 0

Bad bonds: 0 / 963 0.00% Goal: 0%

Bad angles: 0 / 1302 0.00% Goal: <0.1%

Peptide Omegas Cis Prolines: 0 / 3 0.00% Expected: ≤1 per chain, or ≤5%

Low-resolution Criteria CaBLAM outliers 9 7.5% Goal: <1.0%

CA Geometry outliers 4 3.33% Goal: <0.5%

Additional validations Chiral volume outliers 0/142
Waters with clashes 0/0 0.00% See UnDowser table for details
In the two column results, the left column gives the raw count, right column gives the percentage.
* 100^th percentile is the best among structures of comparable resolution; 0^th percentile is the worst. For clashscore the comparative set of structures was selected in 2004, for MolProbity score in 2006.
^{^} MolProbity score combines the clashscore, rotamer, and Ramachandran evaluations into a single score, normalized to be on the same scale as X-ray resolution.
Key to table colors and cutoffs here:

Multi-criterion visualizations

View (78 Kb)

View (2.8 Kb)

Single-criterion visualizations

Clash list (1.6 Kb): View
Ramachandran plot kinemage (412 Kb): View in KiNG | View in NGL | Download
Ramachandran plot PDF (1.7 Mb): View
Ramachandran distribution Z-score analysis (7.2 Kb): View
Chiral volume report (788 bytes): View
Cβ deviation scatter plot (14 Kb): View in KiNG | View in NGL | Download

Summary statistics for m17_5uke_trimmedH.pdb

All-Atom
Contacts Clashscore, all atoms: 22.98 25^th percentile^* (N=1784, all resolutions)

Clashscore is the number of serious steric overlaps (> 0.4 Å) per 1000 atoms.

Protein
Geometry Poor rotamers 12 12.12% Goal: <0.3%

Favored rotamers 80 80.81% Goal: >98%

Ramachandran outliers 4 3.28% Goal: <0.05%

Ramachandran favored 107 87.70% Goal: >98%

Rama distribution Z-score -1.92 ± 0.68 Goal: abs(Z score) < 2

MolProbity score^{^} 3.28 14^th percentile^* (N=27675, 0Å - 99Å)

Cβ deviations >0.25Å 0 0.00% Goal: 0

Bad bonds: 0 / 963 0.00% Goal: 0%

Bad angles: 0 / 1302 0.00% Goal: <0.1%

Peptide Omegas Cis Prolines: 0 / 3 0.00% Expected: ≤1 per chain, or ≤5%

Low-resolution Criteria CaBLAM outliers 10 8.3% Goal: <1.0%

CA Geometry outliers 3 2.50% Goal: <0.5%

Additional validations Chiral volume outliers 0/142
Waters with clashes 0/0 0.00% See UnDowser table for details
In the two column results, the left column gives the raw count, right column gives the percentage.
* 100^th percentile is the best among structures of comparable resolution; 0^th percentile is the worst. For clashscore the comparative set of structures was selected in 2004, for MolProbity score in 2006.
^{^} MolProbity score combines the clashscore, rotamer, and Ramachandran evaluations into a single score, normalized to be on the same scale as X-ray resolution.
Key to table colors and cutoffs here:

Multi-criterion visualizations

View (89 Kb)

View (2.8 Kb)

Single-criterion visualizations

Clash list (1.9 Kb): View
Ramachandran plot kinemage (412 Kb): View in KiNG | View in NGL | Download
Ramachandran plot PDF (1.7 Mb): View
Ramachandran distribution Z-score analysis (7.2 Kb): View
Chiral volume report (788 bytes): View
Cβ deviation scatter plot (14 Kb): View in KiNG | View in NGL | Download

Summary statistics for m18_5uke_trimmedH.pdb

All-Atom
Contacts Clashscore, all atoms: 22.98 25^th percentile^* (N=1784, all resolutions)

Clashscore is the number of serious steric overlaps (> 0.4 Å) per 1000 atoms.

Protein
Geometry Poor rotamers 10 10.10% Goal: <0.3%

Favored rotamers 82 82.83% Goal: >98%

Ramachandran outliers 4 3.28% Goal: <0.05%

Ramachandran favored 105 86.07% Goal: >98%

Rama distribution Z-score -1.91 ± 0.70 Goal: abs(Z score) < 2

MolProbity score^{^} 3.26 15^th percentile^* (N=27675, 0Å - 99Å)

Cβ deviations >0.25Å 0 0.00% Goal: 0

Bad bonds: 0 / 963 0.00% Goal: 0%

Bad angles: 0 / 1302 0.00% Goal: <0.1%

Peptide Omegas Cis Prolines: 0 / 3 0.00% Expected: ≤1 per chain, or ≤5%

Low-resolution Criteria CaBLAM outliers 13 10.8% Goal: <1.0%

CA Geometry outliers 4 3.33% Goal: <0.5%

Additional validations Chiral volume outliers 0/142
Waters with clashes 0/0 0.00% See UnDowser table for details
In the two column results, the left column gives the raw count, right column gives the percentage.
* 100^th percentile is the best among structures of comparable resolution; 0^th percentile is the worst. For clashscore the comparative set of structures was selected in 2004, for MolProbity score in 2006.
^{^} MolProbity score combines the clashscore, rotamer, and Ramachandran evaluations into a single score, normalized to be on the same scale as X-ray resolution.
Key to table colors and cutoffs here:

Multi-criterion visualizations

View (92 Kb)

View (2.8 Kb)

Single-criterion visualizations

Clash list (1.9 Kb): View
Ramachandran plot kinemage (412 Kb): View in KiNG | View in NGL | Download
Ramachandran plot PDF (1.7 Mb): View
Ramachandran distribution Z-score analysis (7.2 Kb): View
Chiral volume report (788 bytes): View
Cβ deviation scatter plot (14 Kb): View in KiNG | View in NGL | Download

Summary statistics for m19_5uke_trimmedH.pdb

All-Atom
Contacts Clashscore, all atoms: 20.84 30^th percentile^* (N=1784, all resolutions)

Clashscore is the number of serious steric overlaps (> 0.4 Å) per 1000 atoms.

Protein
Geometry Poor rotamers 11 11.11% Goal: <0.3%

Favored rotamers 76 76.77% Goal: >98%

Ramachandran outliers 3 2.46% Goal: <0.05%

Ramachandran favored 105 86.07% Goal: >98%

Rama distribution Z-score -1.68 ± 0.73 Goal: abs(Z score) < 2

MolProbity score^{^} 3.25 15^th percentile^* (N=27675, 0Å - 99Å)

Cβ deviations >0.25Å 0 0.00% Goal: 0

Bad bonds: 0 / 963 0.00% Goal: 0%

Bad angles: 0 / 1302 0.00% Goal: <0.1%

Peptide Omegas Cis Prolines: 0 / 3 0.00% Expected: ≤1 per chain, or ≤5%

Low-resolution Criteria CaBLAM outliers 14 11.7% Goal: <1.0%

CA Geometry outliers 4 3.33% Goal: <0.5%

Additional validations Chiral volume outliers 0/142
Waters with clashes 0/0 0.00% See UnDowser table for details
In the two column results, the left column gives the raw count, right column gives the percentage.
* 100^th percentile is the best among structures of comparable resolution; 0^th percentile is the worst. For clashscore the comparative set of structures was selected in 2004, for MolProbity score in 2006.
^{^} MolProbity score combines the clashscore, rotamer, and Ramachandran evaluations into a single score, normalized to be on the same scale as X-ray resolution.
Key to table colors and cutoffs here:

Multi-criterion visualizations

View (87 Kb)

View (2.8 Kb)

Single-criterion visualizations

Clash list (1.8 Kb): View
Ramachandran plot kinemage (412 Kb): View in KiNG | View in NGL | Download
Ramachandran plot PDF (1.7 Mb): View
Ramachandran distribution Z-score analysis (7.2 Kb): View
Chiral volume report (788 bytes): View
Cβ deviation scatter plot (14 Kb): View in KiNG | View in NGL | Download

Summary statistics for m20_5uke_trimmedH.pdb

All-Atom
Contacts Clashscore, all atoms: 25.65 20^th percentile^* (N=1784, all resolutions)

Clashscore is the number of serious steric overlaps (> 0.4 Å) per 1000 atoms.

Protein
Geometry Poor rotamers 9 9.09% Goal: <0.3%

Favored rotamers 80 80.81% Goal: >98%

Ramachandran outliers 2 1.64% Goal: <0.05%

Ramachandran favored 108 88.52% Goal: >98%

Rama distribution Z-score -1.57 ± 0.70 Goal: abs(Z score) < 2

MolProbity score^{^} 3.21 16^th percentile^* (N=27675, 0Å - 99Å)

Cβ deviations >0.25Å 0 0.00% Goal: 0

Bad bonds: 0 / 963 0.00% Goal: 0%

Bad angles: 0 / 1302 0.00% Goal: <0.1%

Peptide Omegas Cis Prolines: 0 / 3 0.00% Expected: ≤1 per chain, or ≤5%

Low-resolution Criteria CaBLAM outliers 9 7.5% Goal: <1.0%

CA Geometry outliers 2 1.67% Goal: <0.5%

Additional validations Chiral volume outliers 0/142
Waters with clashes 0/0 0.00% See UnDowser table for details
In the two column results, the left column gives the raw count, right column gives the percentage.
* 100^th percentile is the best among structures of comparable resolution; 0^th percentile is the worst. For clashscore the comparative set of structures was selected in 2004, for MolProbity score in 2006.
^{^} MolProbity score combines the clashscore, rotamer, and Ramachandran evaluations into a single score, normalized to be on the same scale as X-ray resolution.
Key to table colors and cutoffs here:

Multi-criterion visualizations

View (90 Kb)

View (2.8 Kb)

Single-criterion visualizations

Clash list (2.1 Kb): View
Ramachandran plot kinemage (412 Kb): View in KiNG | View in NGL | Download
Ramachandran plot PDF (1.7 Mb): View
Ramachandran distribution Z-score analysis (7.2 Kb): View
Chiral volume report (788 bytes): View
Cβ deviation scatter plot (14 Kb): View in KiNG | View in NGL | Download

Multi-model multi-criterion kinemage

Note: these kins are often too big to view in the browser. You may need to download it and view it off line.
Multi-criterion kinemage (4.9 Mb): View in KiNG | View in NGL | Download

Multi-model Ramachandran plot

Ramachandran plot PDF (2 Mb): View

Multi-model Ramachandran plot kinemage

Ramachandran plot kinemage (616 Kb): View in KiNG | View in NGL | Download